[Chimera-users] demo made under Linux has bland atoms in Windows

Kenward Vaughan kvaughan at bc.cc.ca.us
Fri Feb 16 16:39:53 PST 2007

On Fri, 2007-02-16 at 15:55 -0800, Elaine Meng wrote:
> Hi Kenward,
> That is certainly unexpected.  To try to figure this out, a few 
> questions:
> on those Windows machines,
> - does manually entering the command "color byelement"  work on the 
> structure(s) in the demo, or on any structures for that matter?
> - do other coloring operations work, within or separate from the demo?

AFAIK things behave normally on the machines (I'm not there right now,
so can't test this, but I've had no trouble in the past).

Using "color byelement" (at the command line) in the middle of the demo
straightened things out at least for the frame being looked at.  I'm
_not_ sure but seem to recall that things got messed up again at a later

I figure I can deal with it by simply adding the command at places where
it is needed, but I'm really curious why it arises at all.

The demo is the "latest" version of the one I sent to you earlier.  I'll
send it under separate cover to you so as to not clutter up the list.
It depends on 2ace.pdb and ach.pdb being in the same directory as the
demo script.


> I don't think we know of any Chimera bug (yet) that would make 
> everything gray. I had a problem once on some oldish Windows computers 
> where everything except "wire" representation was really dark - it was 
> a problem with the graphics hardware and/or driver.
> I could take a look if you want to mail it to me.  I'm not on Windows, 
> however.  We could try it on Windows next week.  Sorry about the 
> travails,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> On Feb 16, 2007, at 2:15 PM, Kenward Vaughan wrote:
> > ...in a fashion, that is.
> >
> > A demo I plan on using at school (a Windows fortress, it is) displays
> > all atoms as grey--no color (by element).  The demo was created on a
> > Linux machine (at my home).
> >
> > :(
> >
> > Any thoughts?
> >
> >
> > Kenward
> > ps. both versions of Chimera are the latest production version (2304).

Dr. Kenward Vaughan                    `:,'~~~~~
Professor of Chemistry                 \;:/
Bakersfield College                    |,;|
1801 Panorama Drive                   / ', \
Bakersfield, CA  93305               / o  O \
http://www2.bc.cc.ca.us/kvaughan    (oOoOOoOo)

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